The effect of Hoffmeister anions Cl−, SO42−, and ClO4− on the structure and morphology of birnessite and cryptomelane-type manganese dioxide nanostructures, produced by the reduction reaction of KMnO4 and MnSO4 in aqueous acidic media, was studied. The syntheses were based on the decomposition of aqueous KMnO4 in presence of HCl for birnessite-type and acidified MnSO4 for cryptomelane-type manganese dioxide under soft hydrothermal conditions. They were characterized using X-ray diffraction (XRD), transmission electron microscopy (TEM), and high-resolution transmission electron microscopy (HRTEM) techniques. XRD patterns show the formation of birnessite for the first synthesis and a mixture of cryptomelane and birnessite-types MnO2 for the second synthesis. XRD data revealed that the Hoffmeister anions have a significant effect on the nanostructures of birnessite. The sulphate ion-treated birnessite has the smallest crystals, whereas the chloride ion-treated birnessite has the largest crystals. Their TEM and HRTEM studies revealed a transformation from nanoplatelet morphology for chloride-treated samples to nanofibrous morphology for sulphate-treated birnessite. For the cryptomelane nanostructures, Hoffmeister anions also show a profound effect on their crystalline structures as determined by XRD analyses revealing a transformation of the cryptomelane phase to birnessite phase of MnO2. This transformation is also supported by TEM and HRTEM studies.